Remains: The Past in the Present
by TomBoyBookGirl
Summary: Sequel to Remains. A body is found, and with it, the truth of Clary's past. When the remains turn out to be those of her mother, she must find out what happened, along with Jace, the team at the Institute, and the brother who abandoned her. But with Armel on the loose, can they find the truth? Or will Clary get lost in her past?
1. Prologue

**I'm back! Yay it's FINALLY up! Cupcake time! I'm SO excited for this fic because there is a lot more change! There will be a lot more moments in Clary and Jace's relationship, and hopefully some Malec in there too. Plus a Sizzy surprise! There will also be some cute family fluff with Jonathan and…. Valentine? Find out! **

**Prologue**

Clary and Jace arrived at the new section of the Institute, their temporary lab until the old one was fixed. Clary raced, well, as best she could, to her temp office to retrieve her lab coat and gloves to start examining the new found remains. Jace walked up to the platform, then stopped, remembering what happened last time. He looked up to see Simon and Isabelle, looking at a computer screen, and a caramel skinned girl with short dark hair and warm brown eyes. "Simon? Izzy?" he said, getting their attention. He gestured to the sensors on the railings, preventing him from entering. "A little help?" Simon, who looked extremely tired, looked up and turned to the dark haired girl. "Maia, can you help Jace?" he asked. Maia, who had been focused on her work, looked up, confused. "Wait, what?" she said. Isabelle rolled her eyes and walked down to the edge of the platform and swiped her card through the slot so Jace could come up. He looked at the body. This one wasn't covered in algae and little bits of flesh like the last one. This one was covered in dusty, dry dirt and the bones were all that was left.

"I'm here!" Clary said, racing up the steps to the platform. She got up and started examining right away. "Female, late thirties early forties. No signs of foul play except some bruising on the femurs and ulnas." she said, after mere seconds of examination. She looked up at Maia, who was placing tissue markers on the skull. "Tell me when you're done Maia, so I can check the tissue markers and Isabelle can do a facial reconstruction." she said. Maia nodded and went back to work. Clary did a little more examination before her phone buzzed. She pulled it out of her pocket and cursed under her breath.

"What?" Isabelle asked, unplugging her Canon T3i camera from the computer and walking up to the remains, taking a few pictures. "I have a meeting with an Art Gallery today,"she said taking off her gloves and putting her phone away. "They want to put one of my painting of guatemala up. I've gotta go." she said running down the steps towards her temp office without even a glance back.

…

Clary walked into her temp office, throwing her lab coat onto the small chair next to the door. She ran to her desk and grabbed a piece of paper with a picture of her painting on it. She cursed under her breath and looked back at the real painting. Jace walked in the door. "What's the rush?" he asked, walking up beside her. Clary sighed. "I need to be there in 10 minutes and I don't know whether to bring the picture or the painting." she said looking back and forth between the two. "Take the picture." Jace said. Clary looked at the picture quickly before sighing. "Alright." she said then turned to Jace. "Can you drive me, please?" Jace smirked. "I don't know…" he said, his tone dripping with sarcasm. Clary crossed her arms and glared at him. "Well, I might just have to steal your car." She raised her hand to revile Jace's car keys. Jace stared wide eyed at her. "How did you..." he asked, digging through his pocket where he put them, only to find them gone.

Clary smirked. "For the world's best FBI agent, you really need to watch where you put your keys." Clary reached into her pocket and pulled out a set of house keys. _Jace's _house keys. "Why'd you take my house keys?" he asked, reaching for them but Clary pulled them back. "So I have leverage." she said. Then Jace caught on. He sighed, being defeated."Fine, I'll drive you." Clary smiled and gave him back his keys. She grabbed the picture and her and Jace walked out of her office.

When they walked passed the observation platform, Maia came running down the steps. "Wait! Clary!" she called. Clary sighed and rolled her eyes. Now _everyone _was calling her that. "Yes Maia?" she asked, turning to face her. "I finished the tissue markers." she said. Clary handed Jace the picture and raced up the steps with Maia, grabbing and slipping on a pair of gloves. Jace stood below the steps, not wanting to set the alarm off again. "I thought you were going to be late?" he called as Clary was reviewing the tissue markers. "I'll be there in a second.." she said trailing into thought. "The depth on the upper maxilla seems a little much to me but good work." Clary said turning to Maia who smiled. "Take this to Isabelle." she told her, taking her gloves off. The two walked down the steps before walking in two separate directions.

Simon walked over to them quickly, delaying their departure even more. "Clary have you seen my microscope trays? I can't find them anywhere." he asked. Clary sighed. "The new shipment came in yesterday. They're in my office." Simon nodded. "Thanks." he was about to walk past them when he stopped and turned to face them. "Why aren't you taking the painting?" He asked, gesturing to the picture. Clary grabbed the picture and ran towards her office. Jace turns to Simon, an exasperated look on his face. "And she's worried about being late."

…

Clary threw the picture down on her small, cluttered desk and walked behind it, grabbing the fairly large painting just behind it. She lifted the corners off the floor and stumbled out of the door, nearly hitting Jace in the process. "Woah," he said, lowering the painting so he could see her face. "You are way too short to be carrying this." he said taking the painting from her. "Be careful! The oil paint might not be dry!" she said, finally letting go. Jace held the painting away from him, making sure he didn't mess up the drying oil paint wasn't getting on his clothes. "Okay," he said, letting out a breath and raising his head over the painting so she could see him. "Can we go _now_?" Clary smiled. "Yes."

Jace turned around and started walking towards the doors when Clary stopped in her tracks. Jace turned to face her, putting the painting against the wall. "What do you need now?" he asked, exasperated. Then he saw her face. Her expression was pained, and unbelieving. "Clary? Are you al-" he didn't get to finish because Clary had already run into Isabelle's office, where the victim's facial reconstruction was displayed. "That's wrong Isabelle!" she yelled. Izzy looked at her in shock. "Wha-" "You got it _wrong_! You made a mistake! It can-n't… it can't-t…" she said trailing off and running off again. "Okay, I'll shut it off!" Isabelle yelled, closing the facial reconstruction.

…

Clary ran up the steps of the examination platform, setting the alarm off on her way up. "Clary!" she heard Jace call to her. She didn't stop. Maia looked up at her. "What is it Clar-" "Where are the artifacts found with the remains?!" Clary yelled. Maia pointed at the table where Simon had been working just before. Clary ran over, grabbed the orange folder and racing back down the steps towards her office.

She ran inside, pushing multiple stacks of paper onto the floor. She opened the folder and pulled out a small glass horse. _This was Jonathans…._ she remembered. She dreaded what she would pull out next. Thankfully it was just a old piece of parchment. She payed no attention to it because most of the ink had faded so the print wasn't legible. Then, she found it. She pulled out a necklace. Silver chain with a orange lily pendant. Her mother got it from her father as a birthday present. She never took it off. Never. That made her theorie all the more real. Jace came in the doorway seeing Clary on the verge of tears, holding the necklace in her small, shaking, pale fingers.

…

The whole group was in Izzy's office, gathered around the large projection screen. Trying to think of what set Clary off. Hodge, Maia, Simon and Isabelle were sitting in silence until Jace walked in. "What happened when Clary came in here?" he asked Isabelle. She grabbed the tablet, connected to the Sizzy-tron. "She freaked when she saw this." Isabelle said, opening the facial reconstruction. Jace's eyes widened at the sight, catching the attention of everyone. "What is it?" Simon asked. "I've seen her before. At Clary's house." he said. Simon and Isabelle exchanged sad glances. They knew who this was. "Good god," Hodge said staring at the screen in disbelief. Jace took a breath. "We just found Clary's mother."

**Dun dun DUN! I bet you all saw that coming! Well that was the prologue, to the sequel to Remains! Until chapter 1, cupcakes to all!**

**-TBBG**


	2. Chapter 1

**Chapter 1 Woo! Thank you all for your follows, favorites and reviews! Like always it make my day that you guys are enjoying this story! The sequel wouldn't even exist if it weren't for you! So here is Chapter 1!**

**Chapter 1**

_Her mother was a florist. She loved flowers. Included them everywhere. She was also an artist. Like Clary, she couldn't get enough. She decided to paint everyone with their favorites. She painted Jonathan with Cattleya Orchids, meaning Mature Charm. Valentine with a red Poppy, meaning Pleasure. He could always make her smile. And Clary with Violets, meaning Faithfulness. Clary painted one for her mother as well. It had orange Day Lily's on it. Her mother's favorite. They symbolised; a Mother's Love. Which confused Clary. Why would she leave? _

_She was in darkness, letting her thoughts run around and around in her head. The orange lily, her parent's laughter, the piano, her brother picking her up and spinning her around the room, laughing. Everything soon turned black, taking the memories away from her. The lily necklace. The only thing left in her vision, began melting away in red drops of blood. Her mother's blood. _"Clary!" _Her breathing picked up, she saw her mother. Her chest had a red stain, growing until it covered her completely. _"Clary!" _The blood cleared and nothing was left but bones. _

"Clary! Wake up!" Clary sat straight up, eyes widened, beads of sweat rolling down her face. She looked over and saw Jace, sitting on the side of her bed. She realised she was in her house, and it was dark outside. "You were having a nightmare," he said calmly, putting a hand on her shoulder. She lay back down on the bed, placing hand over her face, trying to stop the tears. "I'm fine.""she said, trying to sound calm. But she failed. "You were crying in your sleep," he added, rubbing her arm comfortably. "The evidence says otherwise." Clary sighed, taking his hand off her arm and grasping it in hers. "I'm alright." she said, giving him a reassuring glance.

He sighed. "I'll be on the couch if you need me." he said. He stood and was about to leave, but Clary didn't let go of his hand. He turned to face her, to see her on the verge of tears once again. "C-can you stay with me?" she asked. Jace gave her a look. "I don't know," Clary glared at him. "Do you want me to steal your keys again?" she asked. Jace sighed. "Alright, alright I'll stay." Clary moved to the other side of the bed, allowing Jace to climb in beside her. Sh immediately wrapped her arms around him and rested her head on his chest. "Someone's clingy." he mumbled and Clary flicked him. He put hand to his head, and hissed in pain. Clary smiled and looked up at him. Before she could lay back down, Jace lifted her head towards his and kissed her.

She smiled and leaned into the kiss. This is what she needed. An excuse to forget everything else in the world. And just kiss him. Her feeling inside were mixed and scrambled. She wasn't quite sure how she felt about him, but she knew what they had, right now, was right. Jaace pulled away, giving her a kiss on the forehead before hugging her close to him. "You'll get through this." he said, hugging her closer. Clary just stared into space, lost in thought. _But in how many pieces?_

…

Clary shot up in was the same thing over and over. The memories. The lily. The blood. She shook her thoughts away and walked into the kitchen to find Jace, lounging on the couch sipping his coffee. He turned to face her. "Morning." he said, giving her a small smile. She returned it and walked into the kitchen pouring herself a cup of coffee. She had bags under her eyes from the countless times she woke up the night before. She went to pour the coffee, but missed and spilled it all over the small island and her hand, burning herself. She cursed under her breath and ran to the sink, running her hand under the freezing cold water. Jace stood up, grabbing some paper towels and started wiping up the mess. "No, let me clean it up." Clary said walking over from the sink to the island, grabbing some paper towels as she did. "It's fine, let me get it." he replied. "No, you're my guest it's my mess I can handle it!" "Clary," "Pass me another paper towel please." "Clary." "I'll clean it up no need to do my work. I'm fine I'll-" "Clary!" he said, louder so she actually heard him. "You're stressed, you're tired, go sit down."

She calmly obeyed and layed down on the couch, getting lost in thought when the doorbell rang. Clary jumped up instantly. "I'll get it!" she yelled. Jace was still cleaning the kitchen so he let her go. Clary was glad she slept in her clothes so she wouldn't be in front of, whoever this was, in her pajamas. She opened the door to see a man, holding a bouquet of flowers in front of his face. She looked at them. They were purple hyacinth's which meant 'I'm sorry' with a Cattleya Orchid in the middle. She knew all too well what that one ment. It stood for 'Mature Charm'. Jonathans Flower. She took the flowers out of the man's hands so she could see him.

She was soon met by white hair, and emerald green eyes. Just like her mother's. Just like her's. She felt utter shock, then anger. She dropped the flowers to the ground and slapped him across the face. He looked away, then back at her. "I probably deserve that, don't I?" She couldn't fight it. Tears started to fall, and she threw her arms around him. He hugged her back and rested his head on her shoulder. "Hey Clare-Bear." he said quietly. She smiled. She didn't want to forgive him, but he was all she had. She was all he had. She smiled. "Hey Jon."

**Shorter chapter, I know but Jonathan's here! Did you guys like the flower message? There will be more! Flowers will be a BIG role in this Fanfic. Well, eat cupcakes and enjoy!**

**-TBBG**


	3. Chapter 2

**Chapter 2**

**Im back! I won't update for a little bit because exams…. UGH! BUT I have Monday and Tuesday off… I think… so I will try and update then! Okay, enough of my grade 9 problems, here is Chapter 2!**

Clary wiped a few tears away and pulled back from Jonathan, before slapping him, _again_. He felt hands grabbing her wrists and pulling her back. "Okay, no need for violence." said Jace, in his usual sarcastic tone. "It's fine." Jonathan said, holding his cheek. "I deserve it. After all," he looked at Jace for a second then back at Clary. "You shouldn't abandon your 15 year old sister after your parents vanish off the face of the earth."

…

Clary was sitting across from Jonathan on her couch. A angry look on her face. She was feeling too many mixed emotions. She was surprised to see him. She was exasperated that he only decided to show up now. She was happy to see him. She was mad he abandoned her. She was glad he was alive. She was sad her parents were still missing, or dead. Jonathan didn't say a word. He knew she was angry with him. He expected that. And he let her feel that way.

Jace came into the room with a ice pack, wrapped in a cloth for Jonathan. "Thanks." he said, taking the ice pack. "No problem. I know how hard she hits." Jace said with a smirk, sitting next to Clary. Jon smiled at her. "So Clare, you still got those iron fingers?" Clary gave him a shrug, while Jace looked at him, confused. "She would hit me if I annoyed her." he said and Clary threw a book at him. "Ow!" he yelled as the book hit him flat on the chest. Clary gave a small chuckle. "Ör she would throw stuff." he said, winded from the book. Clary lifted another book and raised it above her head. "Okay I'm sorry!" he yelled, holding his hands out in defence.

Clary sat back down on the couch and Jonathan took the ice pack off his face and held it to his chest. "So Jonathan," Jace asked. "Why are you here?" Jonathan took a breath and lowered the ice pack before setting out on the couch. "I came here to tell her I'm sorry." Jace looked at him while Clary leaned back on the couch. "For…?" he asked and Jonathan gave him a sigh. "What are you my kindergarten teacher?" he asked. Jace shrugged and motioned for him to continue. "And because of Dad."

Clary looked up. "D-Dad?" she asked, leaning forward. "But that's impossible Mom and Dad are d-" she froze. She remembered Armel's words that night. _He's very much alive. _But she couldn't say the same for her mother. "They're alive." Jonathan said. Clary's heart burned. He thought they were both alive. "Jon," she said, tears stinging her eyes. "Mom's…" she could barely finish the sentence before the tears came. Jonathan leaned forward, brushing his white hair out of his eyes. "No…" he whispered, not believing it. Clary stood up and walked, well, ran to her brother before crashing down on top of him in tears.

Jace had received a phone call and walked outside, picking the flowers up and slipping them in the mailbox so they wouldn't be crushed. He picked up the phone and waited for what ever he was about to hear. "Hello?" he asked, then Isabelle's voice came on the phone. "_Hey Jace. Is Clary with you?_" she said, her voice sounding worried for her good friend. Jace sighed. "She's alright. I think." he responded. "_You think? Jace what's going on?_" He looked back at the house, hearing Clary's muffled cries and Jonathan trying to calm her. "_Jace I can hear crying. What's going on?_" Jace sighed. How was he supposed to say this? '_Everything's fine! Clary's just feeling mixed emotions right now because she just found her mom's remains and had to tell her older brother who abandoned her when she was 15 and they are now crying on the couch while we are having this conversation.' _That was never going to work. "She'll tell you later, what do you need?"

"_Nothing, really, I… we wanted to see how she was doing aaaand if she was going to come back soon._" she responded. He heard a small conversation in the background, that sounded like Simon, Maia and Hodge. "I don't know…" just then the door opened and Clary and Jonathan walked out. "Who are you talking to?" Clary asked. Her voice was steady but her eyes were a little puffy. "It's Isabe-" he couldn't finish, Clary stole his phone and held it to her ear. "Hey Iz. What's up?" she said quickly, earning a surprised gasp out of Isabelle. "_Clary, hey! We were wondering how you were and, well, when you were planning on coming back._" Clary gave a small smile. "Be there in five." she said then hung up. She gave Jace back his phone and walked over to the car, waiting for it to be unlocked. Jace turned to Jonathan, who had a small smile on his face. "Was she _always_ like this?" he asked and Jonathan chuckled. "She was far worse." Then a rock hit him in the head and they heard Clary call "I heard you!"

**Wow Clary got violent! It's only temporary though… or not. She's just dealing with a whole lot of crap as you can see, man it would suck to be her! And it only gets better! (Note: that was sarcasm.) I might take longer to update, with exams and all PLUS writers block. DONT KILL ME PLEASE! Jace you'll help me right?**

**Jace: Nope.**

**Me: Come on! I let you live in the last one!**

**Jace: Still no.**

**Me: Clary?**

**Clary: No way! Not after all you did, sure I'm still alive but you're torturing me here!**

**Me: Well, maybe I'll just have to put you out of you missery… hehehe**

**Jonathan: Don't you dare! *starts hitting me with a book***

**Me: Okay I'm sorry!**

**Until my bruises heal and I get a sorry cupcake from **_**someone**_**. *cough* Jonathan *cough***

**Jonathan: Not gonna happen.**

**Well, then until I have time. See ya!**

**-TBBG**


	4. Chapter 3

**Chapter 3**

**I return! I got a AWESOME idea for this fanfic and I'm SO excited to write it! (Has anyone else had the problem where it says 'Jace'is spelled wrong? It's weird right?) Well, let's get on with this!**

Clary, Jace and Jonathan arrived at the Institute after a long, awkward car ride. No one talked, the radio was off, it was, well, awkward. Once they arrived, Clary and Jace hopped out of the car, walking up to the Institute while Jonathan lagged behind. He took a moment to take in the scene before him. The Institute, was a large, white brick building, fairly large windows that reflected the morning sun, spreading a bright line across the building. Or, the better half. On the right side of the building, the white brick, was charred black. The top corner of the wall had completely caved in, as well as part of the roof.

He increased his pace to catch up with Jace and Clary, who had already reached the door. Once inside, Clary was attacked by Isabelle. She ran to her friend and jumped on top of her, knocking her to the floor. "Iz!" Clary chuckled, trying to get up off of the floor. Isabelle stood up brushing the dirt off her black skirt and reaching a and down to help Clary off the floor. "Sorry," she muttered before enveloping her friend in a hug. "Are you okay?" Clary nodded, before pulling away. "Isabelle," Clary said stepping to the side so Jonathan was visible. "This is my brother Jon-" she couldn't finish the sentence, because Isabelle had walked over to Jonathan, and punched him square in the nose.

"Iz!" Clary yelled while Simon pulled Isabelle off her brother. Jon held his hand in the air, signaling that he was okay, besides the fact that his nose was bent at an obscure angel and blood was running from it. Jace lifted Jon to his feet, he stumbled slightly, but gained his balance once again. "What was that all about?" Simon asked. He didn't really know who Jonathan was, or what he did. "That son of a bitch abandoned her when she was only _15_!" she said through gritted teeth. She tried to go at him again, but Simon, with the help of Clary and Hodge, who had just walked in, they managed to calm her down. They had enough murders on their hands.

After a lot of explaining, Clary, with the help of Jonathan, explained to everyone her past. That before, was completely off limits. Isabelle was the only one Clary ever told, up until now. If anyone asked about her past, she would ignore them, but once, after Simon asked a few too many questions, she exploded. She yelled in his face and told him to '_shut the fuck up_', which was weird because Clary was usually quiet, calm and rational. (Even if she was a little too rational with some things.) Once Isabelle had calmed down, she was willing to forgive Jonathan. Though, she was still not to bright on the idea of trusting him.

"Jon, could you follow me into my office?" Clary asked, standing up from where she was seated in the caff. Jonathan rose from his seat before following his sister into her office. It was messy, like her room when they were kids, but with alot of boxes and papers,even some human remains from Guatemala. A patella here, a temporal bone there, even a femur just laying on her desk, half buried in a stack of papers. "Nice place you've got here." he said with a hint of sarcasm. Clary walked behind him and shut the door, then locking it.

Jonathan turned to face her, but his expression dropped when he saw her. SHe had a look of anger and sadness on her face. "Clare," he began, backing up slightly as she advanced. "Wha-" "Why did you do it?" she said, her voice was off balance, it sounded like she would cry, but her stern look said otherwise. "How could you leave me? Mom and Dad where gone and you left me." Jon stood there, frozen. He didn't know how he could answer her. "I was fifteen. I was only in grade ten. You were graduating. _Why _did you leave me? I needed you."

Jon took a breath. "I left, for you." Clary looked up into his dark eyes, once thought to be black, turned out to be a dark chocolate brown. "Wha- that doesn't make any sense." she said but Jonathan shushed her. "There is so much you don't understand right now and I am going to explain it all." Clary stood stunned at his statement, she knew so little, and yet she felt like she knew nothing at all, not even her name.

…

"About two days ago, I was in L.A., when I got a letter."

_Jonathan was looking out his apartment window, gazing out on the beach as the wind played with his white hair. He waved at the two teenagers that ran across the white sandy beach, splashing each other with the cool blue waves that ran up and down the shore. Emma and Julian were their names. He met them merely a month ago when he moved into the apartment next to theirs. He sighed. Emma reminded him so much of Clary when she was that age. There was a knock on the door, and he quickly rushed to answer it. _

"_Yes?" he said, opening the door. No one was there, just a letter. He picked it up and walked back inside, taking a seat on the couch before opening the letter. _

"I was expecting a letter from the owner of the apartment, since I was only renting it. That was not what I got." He reached into his pocket and pulled out a folded piece of paper, handing it to Clary.

_C.M.,_

_This is your father. This is important. It's about your sister. Just as I feared, Clermont is back. He's after her because he's the only one he can actually pin-point at the moment. I need you to get to New York as soon as you can. Her life is on the line. But be careful, Clermont could, and will, try to hurt you. You know what he's capable of. I'll be leaving for France in a week. Hopefully Clermont will find out and follow me, leaving you two out of this. I'm sorry I got you two involved. Now all that running had been for nothing. But please, stay safe. _

_V.M._

_Only tell her what you think is necessary. But if she knows about Clermont, you can tell her. Just stay safe._

…

Clary stood there for a moment. "Wait, Clermont? A-as in, _Armel _Clermont?" Jonathan nodded, slowly. "How do you know him?" he asked. Clary sighed, _God I have a lot of explaining to do. _

…

Clary explained what had happened, the murder, Armel, even the bombing and the kidnapping. By the end of it, Jonathan's face was as pale as his hair. "Oh god." he breathed out, running his hands through his hair. Clary sat down on her desk, her flaming red curls forming a curtain around her freckled face. "So, Mom and Dad left, to keep us safe," she said, Jon nodded, pulling his hands out of his hair. "And you left, to keep _me _safe." Jon nodded again, sitting down in the chair close to the door. Clary looked at the letter again. "Who's C.M.?" she asked.

…

"When I was seven, and you were only two, the accident happened."

_Armel Clermont was a killer. Or he used to be. Before his daughter Sayla. But his past, finally caught up to him. Valentine Morgenstern and Daniel Young. Former Soldiers in the Military, now hired Assassins for a man known as 'Spades'. Valentine and Daniel were being hunted by one of 'Spades' rivals, 'Wake'. Armel used to work for 'Wake', but he left to raise his daughter. And now, Valentine and Daniel were sent to kill him. _

_Armel was out with his daughter that day. They were going to the park, when Daniel spotted Armel. They approached him, they wanted to find a way out of their task. They couldn't kill him, not when he had a daughter to look after. Valentine and Daniel knew that all too well, they had kids of their own. That's when all hell broke loose. The man sent to kill Valentine and Daniel went to shoot them and run, but he missed. They moved too quickly. Daniel and Valentine hit the ground, and the bullets hit Sayla. The young girl, no older that eight, long brown hair, blue eyes, gone. In two seconds._

"He told me that the day before he left. But, as for who C.M. is…"

_Valentine needed to hide. He needed to take his family and run. Armel, he was out of the killing game, but now, he had no more reason to stay out. He was back. And he would stop at nothing, to get revenge. Valentine arrived home to his wife and two kids. His son, Christopher, and his daughter Adele. He had this plan ready for months. Just incase something went wrong. They would change their names, move to New York, live a normal life. _

"_Christopher," Valentine, now Trayson Fray, called to his son. The young, white haired boy walked up to his father. "Yes daddy?" he asked. "There is a man, after me. And he wants to hurt you and your sister." he said, kneeling down in front of his son. "So Chris, I want you to forget about Chris. You're Jonathan. Jonathan Fray. You're sister, is Clarissa Fray. If you tell anyone, you will be killing your mother and your sister. Say your name."_

"_Jonathan Fray." "Again." "Jonathan Fray. "Again." They said it together. "Jonathan Fray, Jonathan Fray, Jonathan Fray,_

…

Jonathan Fray." he said. He looked up at Clary, she had tears stinging her eyes. "So, my whole life," she said, her voice sounded like she was about to cry. And she was. "is a lie." Jonathan walked up to her, trying to comfort her, she shoved his hands away. "Don't touch me." she said as calmly as she could and stormed out of her office. "Clare!" Jon called to her, she stopped and turned to face him. "Who?" she asked in an irritated tone. "I don't know _who _you're talking about _Christopher_." she spat, he was taken aback by her tone. "I am Adele Morgenstern, because Clarissa Fray, apparently doesn't even exist!" The tears fell, streaming down her face. She ran outside and crashed onto the concrete, leaning against the charred brick. She heard footsteps, and looked up to see Jace, walking towards her.

"Are you okay?" he asked, leaning down next to her, brushing one of her red curls out of the way. "I don't know." she said, wiping the tears off her face. "I don't even know who I am anymore." Jace tilted her chin up to look her in the eyes. "I know, _exactly_, who you are." he said, wiping away the few tears that escaped her eyes once again. "And who might that be?" she asked, unsure of what he meant. Jace put a hand on either side of her face, their nose's inches apart. "You are Clarissa Fray." he said. Clary looked at him for a moment, his golden eyes staring into hers. "And I won't let _anything _happen to you." /sh looked at him, as if she didn't believe him. "Why?" she asked, and inched closer to him, a few tears escaped her eyes once again but Jace brushed them away. "Because I love you."

The distance between them closed. And while they were lost in their own words,somethign dark had happened. While Jonathan was leaving out the back door of the Institute for some fresh air, little did he know, that a certain someone, was waiting to start another plan to avenge his daughter.

**WHATS GONNA HAPPEN WHATS GONNA HAPPEN!? I DONT KNOW! Sorry for the wait! I was busy and writers block is a real jerk! I have this story planned out! It's just a matter of getting there. Happy (late) Valentines day! Cupcakes to all you lonley people out there! I know how it feels, my younger brother and cousin have freaking girlfriends! What's up with that?! Enough of my problems, I'll see you when I see you!**

**-TBBG**


	5. Chapter 4

**Chapter 4**

**I'm SOOOOOOOOO(Too many O's? Nope.) OOOOOOOOOOOOOOOOO sorry! Second Semester has not been kind! I get SO freaking much science homework it's not even funny! (Plus my science teacher likes to change the correct word to say 'turn off the lights' in French like five times a day. It's not even funny.) Writers block has not been kind. Okay, you guys have been so patient and obviously you don't want a A/N so….. here is chapter 4! **

Clary didn't know how long she'd been there, but she didn't care. Her whole life, even her identity, was a lie. She closed her eyes, letting the soothing feeling of Jace rubbing circles on her knuckles, empty her mind of everything that had happened in the last while. "Are you going to be okay?" Jace asked, bringing her back from her thoughts. She nodded. "Ya," she said, opening her eyes to look at him. "I'm fine." She found comfort in his golden eyes. They seemed… different, from when they first met. Before they were harder to read, like he'd built up walls that he thought no one could ever break. Except for her. Now she could see more of what he'd hidden behind those swirling orbs of liquid gold that no one in a long time had seen. He cared. It shone brightly through his eyes like never before. He'd lost the ones he loved a long time ago, he wasn't going to let that happen again.

"We should probably head back inside." he said, gesturing towards the front door of the Institute. Clar shut her eyes and leaned her head on her shoulder. "But I'm comfy." she said in a tired voice. Jace then stood, making her fall towards the ground, catching herself on her elbow. She looked up at him and he smirked. "Well now you're not." he said. Clary rolled her eyes and reached a hand up to Jace, who took it and lifted her up off the ground. "Hopefully we won't find Isabelle beating Jonathan into a pulp for making you upset earlier." he said as they walked towards the door. When they walked in, they found Simon, Isabelle and Maia lounging around in Isabelle's office. Simon was on his phone, presumably watching Star Wars on Netflix, while Maia and Izzy were chatting while sipping on some coffee.

"Look who finally decided to show up for work." Isabelle said sarcastically, giving Clary a small smile as she entered the room. Clary gave her a small smile, then looked around the room curiously. "Where's Jon?" she asked. "Not in here obviously." Simon said, pulling out his ear buds. "Or Iz would be beating the crap out of him." Isabelle glared at him. "I would not!" she exclaimed. Her friends expressions told her otherwise. she rolled her eyes. "Are we going to sit here and talk about Isabelle beating Clary's brother to a pulp," Maia said before anyone could answer. "Even though he deserves it," Isabelle but in. "Iz! I forgave him! It's over!" Clary exclaimed. Maia rolled her eyes and continued. "_Or_, are we going to find out what happened to Clary's mom?" she finished. Clary smiled gratefully at her. "Well," Jace said, causing everyone to look at him. "The first one _does_ sound fun to watch…" Clary elbowed him in the ribs and Simon snickered. "I'm joking!" he said, holding his ribcage where Clary hit him.

Clary and Maia left to go examine the remains while Simon went back to his office. Jace looked over to see Isabelle doing something on her computer. "Aren't you going to help them?" he asked. Isabelle just kept staring at the screen. "I'm going over the pictures of the remains trying to find possible cause of death…" she trailed off, chuckling at something on the screen. Jace left the office and walked around the corner and peaked into Isabelle's office through the large glass window. She was looking at the pictures, but she was also watching cat vines on the other half of the screen. Jace chuckled and walked towards the examination platform when someone called his name.

"Jace!" he turned around to see Alec, Magnus ho on his heels. "We need you." he said, out of breath. Had he run here or something? "What's u-" "Armel's been spotted." Alec said cutting him off. Jace's eyes widened. "Where?" he asked them. Magnus answered this time. "Woods near Tuckahoe Marble Quarry." They wasted no time heading out to the car and driving, with the lights and siren blaring, to the quarry. Nothing was stopping them.

…

Clary and Maia had been there for hours, examining every bone for the slightest idea of what had happened. So far, nothing. "Should we check the ribs again?" Maia said with a yawn. Clary nodded. It was getting late but she didn't care. She was going to find out what happened. "I heard what Seb did for you." Maia said. Clary stopped and sighed, looking down at the floor. "I remember, at one of our parties, I challenged him to a face of in Call of Duty Zombies and I totally pwned him. I will never forget the look on his face." She added with a smile getting a chuckle out of Clary. "If we can get enough evidence, we might actually be able to catch Armel." Clary said, looking back down at her mother's remains. Her and Maia picked up two to three ribs at a time, examining them closely for nicks and bruises. Nothing. Almost an hour later, it was 11:30 at night and they were getting pretty tired. Clary's eyes were drooping and she rested her head on the table for a minute. Maia however, was having a little trouble standing up straight. She had her elbows on the table, eyes almost completely closed, and wobbled. She took a step to catch herself, but knocked the skull and a tray of alcohol, q-tips and other supplies on the floor.

The loud crash woke the two instantly. "Shit!" Maia mumbled under her breath and leaned down to pick up the q-tips while Clary checked the skull over for injuries. Then she saw it. Inside the skull, was a large red stain, with some kind of mark in the middle of it. "Oh my god." Clary whispered under her breath. Maia looked up at her. "What? Is it fractured?" she asked, looking at the skull for damage. Clary looked at her, shaking her head. "I know cause of death."

Clary and Maia raced to Isabelle's office, skull in hand. Once they reached Isabelles office, they threw the door open and turned on the lights. Isabelle and Simon were curled up together on her couch, but the loud bang of the door hitting the wall and the light surprised them both. Simon shot up, looking around for his glasses while Isabelle fell onto the floor. Maia held back a laugh and bother her and Clary had small grins on their faces. "What the hell!?" Iz asked when she got off the floor. Then she saw who it was and her angered expression softened a little. "What's up?" Simon asked with a yawn. Clary held out the skull, face down, so they could see the inside. "I found cause of death." she stated and Isabelle walked up to get a better look, rubbing the sleep from her eyes. She squinted and looked closer. "My mom died from subdural hematona. Bleeding in th brain."

"I don't see an actual injury." Isabelle said, looking a little deeper inside. "Can you scan the inside and outside and see if it left a mark?" Maia asked. Isabelle rushed to the Sizzy-tron and started it up, getting the scanner set up. Simon groaned and put a pillow over his face. "Mm going back to sleep." he muttered. Maia walked over to the couch and pushed Simon off it onto the floor. He groaned and looked up at Maia, fixing his glasses. Maia smirked. "You're helping whether you like it or not."

**I have plans! Writers block take a hike! I now have 2 fanfics going right now but it's helping my writers block! Cupcakes for EVERYONE! *happy dance!* As usual you guys are fabulous, I will try to update soon!**

**-TBBG**


End file.
